4YS1

Human Aldose Reductase complexed with a ligand with an IDD structure (2) at 1.07 A.

Summary for 4YS1

• Entry DOI: 10.2210/pdb4ys1/pdb
• Related: 1US0 4PUU 4PUW 4Q7B 4QBX 4QR6 4RPQ
• Descriptor: Aldose reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid, ... (4 entities in total)
• Functional Keywords: tim barrel, oxidoreductase, inhibitor, complex
• Biological source: Homo sapiens (Human)
• Cellular location: Cytoplasm: P15121
• Total number of polymer chains: 1
• Total formula weight: 36989.04

Authors

Rechlin, C.,Heine, A.,Klebe, G. (deposition date: 2015-03-16, release date: 2016-03-23, Last modification date: 2024-01-10)

Primary citation

Rechlin, C.,Scheer, F.,Terwesten, F.,Wulsdorf, T.,Pol, E.,Fridh, V.,Toth, P.,Diederich, W.E.,Heine, A.,Klebe, G.
Price for Opening the Transient Specificity Pocket in Human Aldose Reductase upon Ligand Binding: Structural, Thermodynamic, Kinetic, and Computational Analysis.
ACS Chem. Biol., 12:1397-1415, 2017

PubMed Abstract: Insights into the thermodynamic and kinetic signature of the transient opening of a protein-binding pocket resulting from accommodation of suitable substituents attached to a given parent ligand scaffold are presented. As a target, we selected human aldose reductase, an enzyme involved in the development of late-stage diabetic complications. To recognize a large scope of substrate molecules, this reductase opens a transient specificity pocket. The pocket-opening step was studied by X-ray crystallography, microcalorimetry, and surface plasmon resonance using a narrow series of 2-carbamoyl-phenoxy-acetic acid derivatives. Molecular dynamics simulations suggest that pocket opening occurs only once an appropriate substituent is attached to the parent scaffold. Transient pocket opening of the uncomplexed protein is hardly recorded. Hydration-site analysis suggests that up to five water molecules entering the opened pocket cannot stabilize this state. Sole substitution with a benzyl group stabilizes the opened state, and the energetic barrier for opening is estimated to be ∼5 kJ/mol. Additional decoration of the pocket-opening benzyl substituent with a nitro group results in a huge enthalpy-driven potency increase; on the other hand, an isosteric carboxylic acid group reduces the potency 1000-fold, and binding occurs without pocket opening. We suggest a ligand induced-fit mechanism for the pocket-opening step, which, however, does not represent the rate-determining step in binding kinetics.

PubMed: 28287700
DOI: 10.1021/acschembio.7b00062

Experimental method

X-RAY DIFFRACTION (1.07 Å)